how can I get long non coding RNA from RNA-seq data?

[eli]

Hi all,
I have analyzied my RNA-Seq data. I have used this tools:
Download sequences(SRA) from ncbi database.
FastQC (Check quality of sequencing).
Trimmomatic(the quality of each raw library is analyzed and sequencing adapters
and bad quality reads are removed)
I have used paired end datas as input in hisat.
I had htseq count.
I have used deseq2 package in galaxy to get up and dawn genes.
now i dont know how can i get novel lncRNAs?

Need help
Thank you in advance

[jennaj]

Hi @eli

@eli

now i dont know how can i get novel lncRNAs?

Is the goal to find out which lncRNAs are present and differentially expressed in your RNA-seq data? Or to also perform your own lncRNA discovery to use with DE (or other) analysis?

• Known non-coding genomic annotation could be incorporated into the count/differential expression analysis. And may have already been, but perhaps filtered out – it depends on which annotation features were present in your GTF and used to generate counts.

• For lncRNA discovery (and subsequent DE with your RNA-seq data), you’ll need to create genomic annotation data that contains non-coding genomic feature predictions.

Note that genome annotation tools won’t work for larger eukaryotic genomes when working at any public Galaxy server (the analysis will be too large). Update: you can try now in 2025! And that may not even be necessary as there are several non-coding annotation resources already available for many model organisms. For example, Gencode includes lncRNAs for human and mouse in the complete annotation GTFs, and as distinct GTFs: https://www.gencodegenes.org/

GTN Tutorials https://training.galaxyproject.org/training-material/

• Genome Annotation
• Transcriptomics

FAQ: https://galaxyproject.org/support/

• Extended Help for Differential Expression Analysis Tools

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@jennaj

Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

Thanks!

[eli]

thank for your help.
my goal is both of them. The genome I used was zea may.
I recognize up and down genes from deseq2 result.

could you please tell me how can i separate coding and noncoding sequence from deseq2 result?
thank you in advance

[eli]

Thank for your help.

my goal is both of them. The genome I used was zea may.

I recognize up and down genes from deseq2 result.

could you please tell me how can i separate coding and noncoding sequence from deseq2 result?

thank you in advance

[jennaj]

Hi @eli

Check your annotation GTF input – does it include non-coding RNA annotation? If so, that information could be used to filter your differentially expressed genes.

Predicting long non-coding RNA is a non-trivial analysis, but there are several domain-specific Galaxy servers that focus in this area. Many have tutorials, examples, novel tools, linked publications. Some analysis work with RNA-seq data directly (assembly, annotation). To review options, go the Galaxy Platform directly, tab into Public Galaxy servers, and keyword search (example: “rna”).

https://galaxyproject.org/use/

Thanks!

[eli]

Thank you very much for your reply🌸